[BioC] bumphunter DMRs difficulties

[James W. MacDonald]

Hi Giovanni,

I don't know about the number of cores. I share compute cycles with 
co-workers, so can't just hog them all up. A recent bumphunter run I did 
on our shared server (a single multi-core machine with I believe 32 
processors) was:

library(doParallel)
registerDoParallel(cores = 12)
bmps.main <- bumphunter(eset, design.cd, cutoff = 0.99)

Which resulted in something like 2500 bumps and finished in, I don't 
know, say 15-20 minutes?

Best,

Jim


On 2/21/2014 12:21 PM, Giovanni Calice wrote:
> Hi Jim,
>
> the call for bumphunter is:
>
> bumphunter(myGenomicRatioSet, design=designMatrix, cutoff=0.05, 
> B=1000, verbose=TRUE)
>
> I set cutoff to 0.05 not cutoffQ.
> Next bumphunter call I will follow your advice;
> regard to parallelize the process what is your suggestion?
>
> Would it be better to parallelize only on some of the ncores?
>
> Best,
> Giovanni
>
> Laboratory of Preclinical and Translational Research
> IRCCS - CROB Oncology Referral Center of Basilicata
> Rionero in Vulture - Basilicata - Italy
>
>
> 2014-02-21 17:52 GMT+01:00 James W. MacDonald <jmacdon at uw.edu 
> <mailto:jmacdon at uw.edu>>:
>
>     Hi Giovanni,
>
>     You should give the actual call you used for bumphunter, rather
>     than simply saying that you used 'recommended parameters'. It
>     looks like you set cutoffQ to 0.05, which is exactly opposite to
>     what you should be doing. Instead you should be using something
>     like cutoffQ = 0.95.
>
>     Best,
>
>     Jim
>
>
>
>
>     On Friday, February 21, 2014 11:36:32 AM, Giovanni Calice wrote:
>
>         Hi Kasper,
>
>         Thank you very much for the immediate response!
>
>           So,
>           What do you suggest?
>
>         Giovanni
>
>         Laboratory of Preclinical and Translational Research
>         IRCCS - CROB Oncology Referral Center of Basilicata
>         Rionero in Vulture - Basilicata - Italy
>
>
>         2014-02-21 17:27 GMT+01:00 Kasper Daniel Hansen
>         <khansen at jhsph.edu <mailto:khansen at jhsph.edu>>:
>
>
>             On Fri, Feb 21, 2014 at 11:25 AM, Giovanni Calice
>             <giovcalice at gmail.com <mailto:giovcalice at gmail.com>>wrote:
>
>                 273952
>
>
>
>             This is a crazy number of putative bumps
>
>             Kasper
>
>
>                 [[alternative HTML version deleted]]
>
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>     --
>     James W. MacDonald, M.S.
>     Biostatistician
>     University of Washington
>     Environmental and Occupational Health Sciences
>     4225 Roosevelt Way NE, # 100
>     Seattle WA 98105-6099
>
>

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099